Typing of Legionella Isolates in the Genomic Era
Daniel Wüthrich, Helena M.B. Seth-Smith and Adrian Egli
from: Legionellosis Diagnosis and Control in the Genomic Era (Edited by: Jacob Moran-Gilad and Rachel E. Gibbs). Caister Academic Press, U.K. (2020) Pages: 321-336.
Precise typing of Legionella clinical and environmental isolates is vastly important, as L. pneumophila is a highly conserved species with clonal groups such as the sequence type (ST) 1. This chapter discusses the typing of Legionella isolates and with emphasis on the new and advantageous genome-based methods. Previously relied on methods such as serotyping, pulsed-field gel electrophoresis (PFGE) and sequence-based typing (SBT) differentiate between L. pneumophila isolates. However, these techniques are flawed when evaluating closely related L. pneumophila types. This suggests that a new gold-standard is needed for effective surveillance of Legionella and prevention of future outbreaks. With the emergence of next-generation sequencing (NGS) and genomics, boundless conclusions can be drawn from the heightened resolution. The four current techniques constantly being applied to novel situations are core genome MLST (cgMLST), whole genome MLST (wgMLST), core genome SNP-tree, and the whole genome SNP-tree. The broad application of WGS is exemplified with mention of prior outbreak investigations utilizing WGS for analysis in conjunction with epidemiological data in varying scenarios read more ...